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MCL coexpression mm9:883: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000117!3.31e-13!23;CL:0000337!3.31e-13!23;CL:0000540!2.58e-12!33;CL:0000047!2.58e-12!33;CL:0000031!2.58e-12!33;CL:0000404!2.58e-12!33;CL:0000393!6.43e-10!39;CL:0000211!6.43e-10!39;CL:0002319!6.48e-10!43;CL:0000221!9.11e-10!44;CL:0000133!9.11e-10!44;CL:0000055!2.78e-08!49
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!1.80e-17!64;UBERON:0003075!1.80e-17!64;UBERON:0007284!1.80e-17!64;UBERON:0001017!7.28e-17!73;UBERON:0001016!4.97e-16!75;UBERON:0000073!6.49e-15!54;UBERON:0004121!1.66e-14!95;UBERON:0000924!1.66e-14!95;UBERON:0006601!1.66e-14!95;UBERON:0001049!2.41e-14!52;UBERON:0005068!2.41e-14!52;UBERON:0006241!2.41e-14!52;UBERON:0007135!2.41e-14!52;UBERON:0010371!4.66e-14!73;UBERON:0003056!1.69e-13!49;UBERON:0000955!2.34e-11!47;UBERON:0006238!2.34e-11!47;UBERON:0002616!2.52e-11!46;UBERON:0003080!1.48e-10!40;UBERON:0002780!3.62e-10!39;UBERON:0001890!3.62e-10!39;UBERON:0006240!3.62e-10!39;UBERON:0002020!7.61e-10!34;UBERON:0010314!7.81e-10!92;UBERON:0000922!3.15e-08!320;UBERON:0000468!1.54e-07!333;UBERON:0003528!2.75e-07!29;UBERON:0002791!2.75e-07!29;UBERON:0001893!2.75e-07!29
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.84953,0.96259,0.434198,0.260188,1.13872,0.538088,0.173246,0.535519,0.170907,0.494602,0.526159,1.57591,0.550255,0.275867,0,2.9427,0.252772,1.4996,0.29826,0.883862,0.223663,0.549359,0.717658,2.61436,0.577606,0.909128,0.469052,0.303071,0.118137,0.455168,0.843667,1.29258,0.425071,0.276324,2.11044,0.678971,0.522578,0.221921,0.570041,0.256422,0.460258,0.0558565,0.27776,0.209497,0.423266,0.662995,0.484612,0.0447507,0.825035,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,1.27827,0.145699,0.555328,0.823643,1.49002,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.236196,1.03623,1.98853,0.813951,0.839631,0.651651,0.806481,0.336166,0.530481,0.759925,0.612313,0.167672,2.12473,5.69681,4.56391,0.757533,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,2.2295,0.859272,0.663249,2.26041,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,1.59446,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,1.35445,0.437894,0.743872,0.238599,1.04163,2.78555,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,5.02266,2.7384,0.461647,1.18819,2.01886,3.53491,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,0.766041,0.780212,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,1.03572,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,1.2562,0.524587,0.842217
|tfbs_overrepresentation_jaspar=MA0003.1;2.21188,MA0004.1;0.434673,MA0006.1;0.747445,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;3.49148,MA0017.1;0.296816,MA0019.1;0.688051,MA0024.1;1.93095,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.769859,MA0029.1;0.804619,MA0030.1;0.811181,MA0031.1;0.775627,MA0038.1;0.577528,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;0.102483,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.0283571,MA0056.1;0,MA0057.1;0.31126,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;0.574356,MA0061.1;5.29701,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;1.61305,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;7.58054,MA0074.1;0.531046,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.375851,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;2.36189,MA0089.1;0,MA0090.1;0.401197,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;0.289361,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;3.50519,MA0103.1;0.307078,MA0105.1;2.60123,MA0106.1;0.626997,MA0107.1;5.08051,MA0108.2;0.710846,MA0109.1;0,MA0111.1;0.415012,MA0113.1;0.598933,MA0114.1;0.222763,MA0115.1;0.969632,MA0116.1;1.36991,MA0117.1;0.937363,MA0119.1;0.362692,MA0122.1;0.957212,MA0124.1;1.16127,MA0125.1;1.0872,MA0130.1;0,MA0131.1;0.683521,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;0.550755,MA0139.1;1.55504,MA0140.1;0.519484,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;0.0701568,MA0146.1;1.31232,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;1.36227,MA0035.2;0.524137,MA0039.2;1.07211,MA0138.2;0.675599,MA0002.2;0.172399,MA0137.2;0.32312,MA0104.2;0.54394,MA0047.2;0.576767,MA0112.2;0.2464,MA0065.2;0.528619,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.677425,MA0155.1;0.275377,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;0.453546,MA0161.1;0,MA0162.1;1.05113,MA0163.1;1.79588,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;2.62627,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.643936,MA0442.1;0
}}

Latest revision as of 16:02, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:102180696..102180760,-p2@Ubtf
Mm9::chr11:94871166..94871204,+p2@Samd14
Mm9::chr11:94871212..94871233,+p4@Samd14
Mm9::chr11:94871250..94871261,+p11@Samd14
Mm9::chr11:94871280..94871343,+p1@Samd14
Mm9::chr11:94871558..94871590,+p5@Samd14
Mm9::chr11:94871607..94871639,-p@chr11:94871607..94871639
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Mm9::chrX:90920427..90920500,+p1@Pcyt1b


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0004105choline-phosphate cytidylyltransferase activity0.0179691565596517
GO:0001541ovarian follicle development0.0409124068227524
GO:0022601menstrual cycle phase0.0409124068227524
GO:0022602menstrual cycle process0.0409124068227524
GO:0008585female gonad development0.0409124068227524
GO:0046545development of primary female sexual characteristics0.0409124068227524
GO:0046660female sex differentiation0.0409124068227524
GO:0042698menstrual cycle0.0409124068227524
GO:0008406gonad development0.0409124068227524
GO:0048608reproductive structure development0.0409124068227524
GO:0045137development of primary sexual characteristics0.0409124068227524
GO:0008654phospholipid biosynthetic process0.0409124068227524
GO:0048609reproductive process in a multicellular organism0.0409124068227524
GO:0032504multicellular organism reproduction0.0409124068227524
GO:0046467membrane lipid biosynthetic process0.0409124068227524
GO:0007548sex differentiation0.0409124068227524
GO:0003006reproductive developmental process0.0453468041274223



Relative expression of the co-expression cluster over median <br>Analyst:




Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neurectoderm1.80e-1764
neural plate1.80e-1764
presumptive neural plate1.80e-1764
central nervous system7.28e-1773
nervous system4.97e-1675
regional part of nervous system6.49e-1554
ectoderm-derived structure1.66e-1495
ectoderm1.66e-1495
presumptive ectoderm1.66e-1495
neural tube2.41e-1452
neural rod2.41e-1452
future spinal cord2.41e-1452
neural keel2.41e-1452
ecto-epithelium4.66e-1473
pre-chordal neural plate1.69e-1349
brain2.34e-1147
future brain2.34e-1147
regional part of brain2.52e-1146
anterior neural tube1.48e-1040
regional part of forebrain3.62e-1039
forebrain3.62e-1039
future forebrain3.62e-1039
gray matter7.61e-1034
structure with developmental contribution from neural crest7.81e-1092
embryo3.15e-08320
multi-cellular organism1.54e-07333
brain grey matter2.75e-0729
regional part of telencephalon2.75e-0729
telencephalon2.75e-0729


TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs




JASPAR motifs


Motifs-log10(p-value)
MA0003.12.21188
MA0004.10.434673
MA0006.10.747445
MA0007.10.419994
MA0009.10.870101
MA0014.13.49148
MA0017.10.296816
MA0019.10.688051
MA0024.11.93095
MA0025.11.10341
MA0027.12.51754
MA0028.10.769859
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.102483
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.0283571
MA0056.10
MA0057.10.31126
MA0058.10.341628
MA0059.10.353484
MA0060.10.574356
MA0061.15.29701
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.11.61305
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.17.58054
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.12.36189
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.13.50519
MA0103.10.307078
MA0105.12.60123
MA0106.10.626997
MA0107.15.08051
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.11.36991
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.11.55504
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.0701568
MA0146.11.31232
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.21.36227
MA0035.20.524137
MA0039.21.07211
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.20.54394
MA0047.20.576767
MA0112.20.2464
MA0065.20.528619
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.677425
MA0155.10.275377
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.11.05113
MA0163.11.79588
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.22.62627
MA0102.21.59466
MA0258.10.210437
MA0259.10.643936
MA0442.10
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